| Summary: | Investigating hypoxia tolerance and growth trait single nucleotide polymorphisms (SNPs) in <i>Macrobrachium nipponense</i> is conducive to cultivating prawns with hypoxia tolerance and good growth characteristics. The glutathione S-transferase-2 gene (<i>GST-2</i>) has been shown to regulate hypoxia responses in <i>M. nipponense</i>. In this study, we identified a single <i>GST-2</i> SNP in <i>M. nipponense</i>, and analyzed its regulatory relationship with hypoxia tolerance and growth. The <i>GST-2</i> sequence was amplified with a polymerase chain reaction from 197 “Taihu Lake No. 3”, “Taihu Lake No. 2”, and Pearl River population samples to identify SNP loci. The full-length <i>Mn-GST2</i> sequence was 2317 bp, including three exons and two introns. In total, 38 candidate SNP loci were identified from <i>GST-2</i> using Mega11.0 comparisons, with most loci moderately polymorphic in terms of genetic diversity. Locus genotypes were also analyzed, and basic genetic parameters for loci were calculated using Popgene32 and <i>PIC_CALC</i>. The expected heterozygosity of the 38 SNP loci ranged from 0.2334 to 0.4997, with an average of 0.4107, while observed heterozygosity ranged from 0.1929 to 0.4721, with an average of 0.3401. The polymorphic information content ranged from 0.21 to 0.37. From SPSS analyses, the G+256A locus was significantly correlated with hypoxia tolerance across all three <i>M. nipponense</i> populations, while the SNP loci A+261C, C+898T, A+1370C, and G+1373T were significantly associated with growth traits. Further analyses revealed that the T+2017C locus was significantly correlated with hypoxia tolerance in “Taihu Lake No. 2” populations, G+256A, A+808T, C+1032T, and A+1530G loci were significantly correlated with hypoxia tolerance in “Taihu Lake No. 3” populations, while no SNP loci were correlated with hypoxia tolerance in Pearl River populations. A+1370C and G+1373T loci, which were associated with growth traits, exhibited a high degree of linkage disequilibrium (r<sup>2</sup> = 0.89 and r<sup>2</sup> > 0.8), suggesting potential genetic linkage. Our data suggest associations between hypoxia tolerance and growth trait SNP loci in <i>M. nipponense</i>, and provide valuable evidence for the genetic improvement of growth and hypoxia tolerance in this prawn species.
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